Dear Amber users,
I am a novice user with Antechamber. I have a system in which the ligand (76 atoms, with netcharge -1) is covalently connected to the protein (CYS:SG).
I am interested in generating a parameter file for protein+ligand (complex) . I could generate .prmtop and .inpcrd files for the ligand separately. The problem occurs when I try for the complex!
Used pd4amber —reduce , [removed ligand coord] and added a hydrogen (for protonation) and a capping hydrogen (H33) > ligand-capped.pdb : Netcharge -1 /singlet
During the parametrization of the ligand (a non-standard residue) :
antechamber -i lig.log -fi gout -fo ac -o lig.ac -c resp -nc -1 -rn LIG -at gaff
I have prepgen file
[to remove capping H and to tell that it will be connected to CYS of the protein]
Lig.mc
HEAD_GROUP C24
OMIT_NAME H33
PRE_HEAD_TYPE SG
CHARGE -1.0
prepgen -i lig.ac -m Lig.mc -o lig.prepin -f int (I get NEWPDB.PDB , using this as a reference PDB for ligand)
parmchk -i lig.prepin -f prepi -o lig.frcmod
In leap:
source leaprc.gaff
source leaper.protein.ff14SB
Loadamberprep lig.prepin
Loadamberparams lig.frcmod
x = loadpdb complex.pdb
desc x.297.C24. (of ligand)
desc x.2.SG. (of protein: (tleap adds additional H, filling the valence of CYS 2:SG))
bond x.297.C24 x.2.SG
saveoff x complex.lib
Loadoff complex.lib
saveamberparm x complex.prmtop complex.inpcrd
I get an error saying atomtypes are missing. I also manually edited the PDB (the ligand part) with no success . I am not sure, if my procedure was correct.
Also, I would like to know the protocol for changing the atom type of subset of atoms (ligand) in a complex.pdb Is the bonding step required (I do it because, in the prepgen, after omitting the H33, it said use bond command to bond) given that I load a complex.pdb (where the protein and ligand are bonded)
Kindly help.
Thank you,
Sincerely,
Sivasudhan R
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Received on Mon Feb 12 2018 - 23:30:07 PST
